On the Coevolution of Transposable Elements and Plant Genomes

Table 1

Known TE proportions in plant genomes when various authors provide different values, the range is given. Inconsistent estimates of TE content result from incomplete genomic representation and/or varying bioinformatical approaches. Examination of complete genomes and application of the same TE discovery pipeline is therefore essential for comparative analyses on intra- and interspecies level. No data on TE content is available for gymnosperms, and angiosperms with large genomes (>2.4 Gbp) are underrepresented. In most genomes, Helitrons were not surveyed appropriately.

Species	Predominant fertilization	Genome size (Gbp)	TE content (%)	DNA transposon content (%)	Retrotransposon content (%)	Genomic fraction examined	References
Arabidopsis thaliana	S	0.125	6–15.36	2-3	4	Complete/draft genome	[12, 25, 32]
Arabidopsis lyrata	C	0.207	23.48	ns	ns	Complete/draft genome	[12, 73]
Brachypodium distachyon	S	0.272	26.17	4.77	21.4	Complete/draft genome	[74]
Carica papaya	C	0.372	51.9	ns	ns	Complete/draft genome	[75]
Cucumis melo	C	0.454	8.13	0.93	7.2	BAC clones (6.7 Mbp)	[76]
Oryza sativa	S	0.472	35	ns	17	Complete chr. 10; complete/draft genome	[24, 39]
Lotus japonicus	S	0.472	30.8	0.97–8.1	10.4–19.23	TAC clones (32.4 Mbp); 2/3 genome	[8, 77]
Medicago truncaluta	S	0.475	38	ns	9.6*	BAC clones (0.233 Mbp)	[40, 78]
Populus trichocarpa	C	0.485	42	2.5**	10.3**	Complete/draft genome	[79]
Vitis vinifera	S	0.487–0.505	21.5–41.4	1.98	20	Complete/draft genome	[41, 80, 81]
Brassica oleracea	C	0.6	20	6	14	Complete/draft genome	[32]
Sorghum bicolor	S	0.73	62.5–59	7.5/17	55/42	Complete/draft genome	[34, 82]
Glycine max	S	1.1	58	16	42	Complete/draft genome (3.42 Mbp)	[38, 83]
Gossypium herbaceum	S	1.667	52.1	<0.1	52	Small insert genomic library (3.42 Mbp)	[84]
Zea mays	C	2.3	85	8.6	75	Complete/draft genome	[29]
Aegilops tauschii	S	4.988	68.2	13.3	53.5	Small insert genomic library (2.911 Mbp)	[38, 85]
Hordeum vulgare	S	5.7	88.1	ns	ns	BAC clones (0.44 Mbp)	[86]
Secale cereale	C	8.093	69.3	5	64.3	BAC clones (2.033 Mbp)	[38, 87]

S—self-pollination; C—cross-pollination; ns—not specified; *only full-length LTR retrotransposons analysed; **only TEs with homology to known repeat elements considered.